Metadata-Version: 1.2
Name: clarite
Version: 1.1.1
Summary: CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures
Home-page: https://github.com/HallLab/clarite-python
Author: Hall Lab
Author-email: mah546@psu.edu
License: BSD (3-clause)
Description: ===============================
        CLARITE
        ===============================
        
        .. image:: https://img.shields.io/travis/HallLab/clarite-python.svg
                :target: https://travis-ci.org/HallLab/clarite-python
        
        .. image:: https://readthedocs.org/projects/clarite-python/badge/?version=latest
                :target: https://clarite-python.readthedocs.io/en/latest/
        
        .. image:: https://img.shields.io/pypi/v/clarite.svg
                :target: https://pypi.python.org/pypi/clarite
        
        .. image:: docs/source/_static/clarite_logo.png
        
        CLeaning to Analysis: Reproducibility-based Interface for Traits and Exposures
        ==============================================================================
        
        * Free software: 3-clause BSD license
        * Documentation: https://www.hall-lab.org/clarite-python/.
        
        Installation
        ------------
        
        In order to use the *ewas_r* function, R must be installed along with the *survey* library.
        This can be done manually or using Conda:
        
        Manually
        ^^^^^^^^
        
        1. Install R and ensure it is accessible from the command line.  You may need to add its location to the PATH environmental variable.
        2. Use *install.packages* in R to install the *survey* library.
        
        Using Conda
        ^^^^^^^^^^^
        
        1. Create and activate a conda environment with python 3.6 or 3.7::
        
            $ conda create -n clarite python=3.7
            $ conda activate clarite
        
        2. Install rpy2 (optional). CLARITE has a version of the EWAS function that calls R code using the *survey* library::
        
            $ conda install -c conda-forge rpy2
            $ conda install -c bioconda r-survey
        
        3. Install CLARITE::
        
            $ pip install clarite
            
        Citing CLARITE
        ^^^^^^^^^^^^^^
        
        1.
        Lucas AM, et al (2019)
        `CLARITE facilitates the quality control and analysis process for EWAS of metabolic-related traits. <https://www.frontiersin.org/article/10.3389/fgene.2019.01240>`_
        *Frontiers in Genetics*: 10, 1240
        
        2.
        Passero K, et al (2020)
        `Phenome-wide association studies on cardiovascular health and fatty acids considering phenotype quality control practices for epidemiological data. <https://www.worldscientific.com/doi/abs/10.1142/9789811215636_0058>`_
        *Pacific Symposium on Biocomputing*: 25, 659
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.6
